A comparison between the binding modes of a substrate and inhibitor to papain as observed in complex crystal structures

1990 ◽  
Vol 171 (2) ◽  
pp. 711-716 ◽  
Author(s):  
Daisuke Yamamoto ◽  
Toshimasa Ishida ◽  
Masatoshi Inoue
2021 ◽  
Author(s):  
Mirko M Maksimainen ◽  
Sudarshan Murthy ◽  
Sven T Sowa ◽  
Albert Galera-Prat ◽  
Elena Rolina ◽  
...  

The scaffold of TIQ-A, a previously known inhibitor of human poly-ADP-ribosyltransferase PARP1, was utilized to develop inhibitors against human mono-ADP-ribosyltransferases through structure-guided design and activity profiling. By supplementing the TIQ-A scaffold with small structural changes, based on a PARP10 inhibitor OUL35, selectivity changed from poly-ADP-ribosyltransferases towards mono-ADP-ribosyltransferases. Binding modes of analogs were experimentally verified by determining complex crystal structures with mono-ADP-ribosyltransferase PARP15 and with poly-ADP-ribosyltransferase TNKS2. The best analogs of the study achieved 10-20-fold selectivity towards mono-ADP-ribosyltransferases PARP10 and PARP15 while maintaining micromolar potencies. The work demonstrates a route to differentiate compound selectivity between mono- and poly-ribosyltransferases of the human ARTD family.


2016 ◽  
Vol 69 (11-13) ◽  
pp. 2015-2023 ◽  
Author(s):  
Shaikh M. Mobin ◽  
Mohd. Tauqeer ◽  
Akbar Mohammad ◽  
Veenu Mishra ◽  
Pratibha Kumari

2014 ◽  
Vol 70 (a1) ◽  
pp. C1793-C1793
Author(s):  
Paul Rowland ◽  
Onkar SINGH ◽  
Leila Ross ◽  
Francisco Gamo ◽  
Maria Lafuente-Monasterio ◽  
...  

Malaria is a preventable and treatable disease, yet annually there are still hundreds of thousands of malaria-related deaths. The disease is caused by infection with mosquito-borne Plasmodium parasites. With hundreds of millions of cases each year there is a very high potential for drug resistance and this has compromised many existing therapies. One target under investigation is the enzyme dihydroorotate dehydrogenase (DHODH) which catalyses the rate-limiting step of pyrimidine biosynthesis and is an essential enzyme in the malaria parasite. There are currently several Plasmodium-selective DHODH inhibitors under development. To investigate the potential for drug resistance against DHODH inhibitors in vitro resistance selections were carried out using known inhibitors from different structural classes [1]. These studies identified point mutations in the drug binding site which lead to reduced sensitivity to the inhibitors, and in some cases increased sensitivity to a different inhibitor, suggesting a novel combination therapy approach to combat resistance. To help understand the significance of the inhibitor binding site mutations we determined the crystal structures of P. falciparum DHODH in complex with the inhibitors Genz-669178, IDI-6253 and IDI-6273. Co-crystallisation experiments led to a new crystal form in each case. Here we describe the crystal structures, the binding modes of the inhibitors and the great flexibility of the binding site, which is able to adjust to accommodate different inhibitor series. The structural role of the resistance mutations is also discussed.


2021 ◽  
Author(s):  
Lewis Turner ◽  
Alexander Lund Nielsen ◽  
Lucy Lin ◽  
Antonio J. Campedelli ◽  
Nicholas Silvaggi ◽  
...  

We have used crystal structures and molecular modeling to evaluate inhibitor binding modes and design a series of compounds to take advantage of a new, cryptic, hydrophobic sub-pocket. This is a classical SBDD approach to improving enzyme/inhibitor interactions.


I shall concentrate upon reviewing the important recent change in our appreciation of the facts of supercooling which has been brought about particularly by the work of Turnbull at the General Electric Research Laboratory in Schenectady. I suppose that most of us, talking about supercooling a couple of years ago, would have divided substances into two classes, one with simple crystal structures like gold, and all the other ‘good’ metals on the one hand, and those with complex crystal structures, such as glycerol and the silicates on the other; saying that whereas the latter class can be very much supercooled, and will form glasses, the former class can only be supercooled a very few degrees. Then we would have added that there are some ‘ bad ’ metals, with moderately complex crystal structures, such as antimony or bismuth, which can be supercooled some tens of degrees, forming an intermediate class. I think we would then have added that this is quite comprehensible. In particular, that the X-ray diffraction patterns of the monatomic liquids show us that most of the atoms have the right numbers of nearest neighbours in a first co-ordination shell, all ready in place to start the growth of a crystal; which readily explains why these substances cannot be supercooled very much—a nice simple experimental fact, with a straightforward theoretical interpretation—and both are wrong.


2009 ◽  
Vol 106 (37) ◽  
pp. 15616-15621 ◽  
Author(s):  
Masataka Umitsu ◽  
Hiroshi Nishimasu ◽  
Akiko Noma ◽  
Tsutomu Suzuki ◽  
Ryuichiro Ishitani ◽  
...  

S-adenosylmethionine (AdoMet) is a methyl donor used by a wide variety of methyltransferases, and it is also used as the source of an α-amino-α-carboxypropyl (“acp”) group by several enzymes. tRNA-yW synthesizing enzyme-2 (TYW2) is involved in the biogenesis of a hypermodified nucleotide, wybutosine (yW), and it catalyzes the transfer of the “acp” group from AdoMet to the C7 position of the imG-14 base, a yW precursor. This modified nucleoside yW is exclusively located at position 37 of eukaryotic tRNAPhe, and it ensures the anticodon-codon pairing on the ribosomal decoding site. Although this “acp” group has a significant role in preventing decoding frame shifts, the mechanism of the “acp” group transfer by TYW2 remains unresolved. Here we report the crystal structures and functional analyses of two archaeal homologs of TYW2 from Pyrococcus horikoshii and Methanococcus jannaschii. The in vitro mass spectrometric and radioisotope-labeling analyses confirmed that these archaeal TYW2 homologues have the same activity as yeast TYW2. The crystal structures verified that the archaeal TYW2 contains a canonical class-I methyltransferase (MTase) fold. However, their AdoMet-bound structures revealed distinctive AdoMet-binding modes, in which the “acp” group, instead of the methyl group, of AdoMet is directed to the substrate binding pocket. Our findings, which were confirmed by extensive mutagenesis studies, explain why TYW2 transfers the “acp” group, and not the methyl group, from AdoMet to the nucleobase.


Author(s):  
John A. Tossell ◽  
David J. Vaughan

The early descriptions of chemical bonding in minerals and geological materials utilized purely ionic models. Crystals were regarded as being made up of charged atoms or ions that could be represented by spheres of a particular radius. Based on interatomic distances obtained from the early work on crystal structures, ionic radii were calculated for the alkali halides (Wasastjerna, 1923) and then for many elements of geochemical interest by Goldschmidt (1926). Modifications to these radius values by Pauling (1927), and others took account of such factors as different coordination numbers and their effects on radii. The widespread adoption of ionic models by geochemists resulted both from the simplicity and ease of application of these models and from the success of rules based upon them. Pauling’s rules (1929) enabled the complex crystal structures of mineral groups such as the silicates to be understood and to a limited extent be predicted; Goldschmidt’s rules (1937) to some degree enabled the distribution of elements between mineral phases or mineral and melt to be understood and predicted. Such rules are further discussed in later chapters. Ionic approaches have also been used more recently in attempts to simulate the structures of complex solids, a topic discussed in detail in Chapter 3. Chemical bonding theory has, of course, been an important component of geochemistry and mineralogy since their inception. Any field with a base of experimental data as broad as that of mineralogy is critically dependent upon theory to give order to the data and to suggest priorities for the accumulation of new data. Just as the bond with predominantly ionic character was the first to be quantitatively understood within solidstate science, the ionic bonding model was the first used to interpret mineral properties. Indeed, modern studies described herein indicate that structural and energetic properties of some minerals may be adequately understood using this model. However, there are numerous indications that an ionic model is inadequate to explain many mineral properties. It also appears that some properties that may be rationalized within an ionic model may also be rationalized assuming other limiting bond types.


2019 ◽  
Vol 104 (7) ◽  
pp. 966-972 ◽  
Author(s):  
J.P. Hirth ◽  
Jian Wang ◽  
Greg Hirth

Abstract A topological model (TM) is presented for the complex crystal structures characteristic of some minerals. We introduce a tractable method for applying the TM to characterize defects in these complex materials. Specifically, we illustrate how structural groups, each with a motif containing multiple atoms, provide lattices and structures that are useful in describing dislocations and disconnections in interfaces. Simplified methods for determining the shuffles that accompany disconnection motion are also described. We illustrate the model for twinning in albite owing to its potential application for constraining the rheological properties of the crust at conditions near the brittle-plastic transition, where plagioclase is a major constituent of common rock types. While deformation twins in plagioclase are often observed in crustal rocks, the interpretation of the stress states at which they form has not advanced. The concept of structural groups makes an analysis of the twinning process easier in complex minerals and explicitly predicts the interface structure of the deformation twins.


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